7CNT | pdb_00007cnt

Structure of 2,5-dihydroxypridine Dioxygenase from Pseudomonas putida KT2440 in complex with product N-formylmaleamic acid formed via in crystallo reaction with 2,5-dihydroxypridine

PDB DOI: https://doi.org/10.2210/pdb7CNT/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida KT2440
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-08-03 Released: 2020-12-16
Deposition Author(s): Liu, G.Q., Tang, H.Z.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.267 (Depositor), 0.270 (DCC)
R-Value Work:
0.211 (Depositor), 0.220 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7CNT

This is version 1.1 of the entry. See complete history.

Literature

2,5-dihydroxypridine Dioxygenase in complex with 2,5-dihydroxypridine and product N-formylmaleamic acid

Liu, G.Q., Tang, H.Z.

(2020) Nat Commun

Macromolecule Content

Total Structure Weight: 247.25 kDa
Atom Count: 16,612
Modeled Residue Count: 2,088
Deposited Residue Count: 2,178
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,5-dihydroxypyridine 5,6-dioxygenase	A, B, C, D, E A, B, C, D, E, F	363	Pseudomonas putida KT2440	Mutation(s): 0 Gene Names: nicX, PP_3945 EC: 1.13.11.9
UniProt
Find proteins for Q88FY1 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88FY1 Go to UniProtKB: Q88FY1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q88FY1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE2 (Subject of Investigation/LOI) Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain K [auth E] SDF format, chain L [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain K [auth E] MOL2 format, chain L [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D] mmCIF format, chain K [auth E] mmCIF format, chain L [auth F]	G [auth A] H [auth B] I [auth C] J [auth D] K [auth E] G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.267 (Depositor), 0.270 (DCC)
R-Value Work: 0.211 (Depositor), 0.220 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.885	α = 90
b = 125.916	β = 90
c = 144.129	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2020-12-16
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Database references, Structure summary

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